read_plink {hibayes}

data load

Description

To load plink binary data

Usage

read_plink(
  bfile = "",
  maxLine = 10000,
  impute = TRUE,
  mode = c("A", "D"),
  out = NULL,
  threads = 4
)

Arguments

bfile

character, prefix of Plink binary format data.

maxLine

number, set the number of lines to read at a time.

impute

logical, whether to impute missing values in genotype by major alleles.

mode

"A" or "D", additive effect or dominant effect.

out

character, path and prefix of output file

threads

number, the number of used threads for parallel process

Value

four files will be generated in the directed folder: "xx.desc", "xx.bin", "xx.id, "xx.map", where 'xx' is the prefix of the argument 'out', the memory-mapping files can be fast loaded into memory by 'geno = attach.big.matrix("xx.desc")'. Note that hibayes will code the genotype A1A1 as 2, A1A2 as 1, and A2A2 as 0, where A1 is the first allele of each marker in ".bim" file, therefore the estimated effect size is on A1 allele, users should pay attention to it when a process involves marker effect.

Examples

bfile_path = system.file("extdata", "demo", package = "hibayes")
data = read_plink(bfile_path, out=tempfile(), mode="A")
fam = data$fam
geno = data$geno
map = data$map